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Journal of Archaeological Science 32 (2005) 331–336
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Contamination controls when preparing archaeological
remains for ancient DNA analysis
Dongya Y. Yang), Kathy Watt
Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, 8888 University Drive,
Burnaby, British Columbia, Canada V5A 1S6
Received 18 August 2004; received in revised form 20 September 2004
Abstract
Contamination is of utmost concern when working with ancient DNA as it easily leads to false positive results. The best way to
prevent or minimize contamination is to start precautionary measures as early as possible, ideally commencing with sample
collection and preparation by field archaeologists. This paper discusses the nature of contamination in ancient DNA studies and
offers some practical guidelines as to how archaeologists in the field can ‘‘clean-collect’’ samples for ancient DNA analysis. Methods
for preparing contaminated samples from museum collections for ancient DNA analysis are also discussed.
Ó 2004 Elsevier Ltd. All rights reserved.
Keywords: Ancient DNA; Archaeological remains; Contamination control; Sample preparation
1. Introduction
The analysis of ancient DNA provides archaeologists
and anthropologists with innovative ways to study the
past [14,15,22,28]. Since it was first applied to Egyptian
mummified materials in 1985 [24], ancient DNA analysis
of archaeological remains has generated many new
insights into important archaeological and anthropological questions regarding human evolution and
population affinities [7,17,23,31], kinship determination
[12], diagnosis of human genetic and infectious diseases
[19,32], domestication of animal and plant species [3,33]
and subsistence practices of past human populations
[20,27,36].
The applicability of ancient DNA to archaeology and
anthropology, however, can be adversely affected by
) Corresponding author. Tel.: C1 604 291 4651; fax: C1 604 291
5666.
E-mail address: [email protected] (D.Y. Yang).
0305-4403/$ - see front matter Ó 2004 Elsevier Ltd. All rights reserved.
doi:10.1016/j.jas.2004.09.008
difficulties associated with the ancient DNA technique
itself [11,16]. Besides DNA degradation in ancient
remains that may leave no intact DNA molecules,
contamination with modern DNA is of paramount
concern as it can easily lead to false results. Contamination controls (i.e. strict precautions and measures)
need to be exercised to prevent or minimize such
contamination. Although there has been much discussion regarding contamination controls among ancient
DNA researchers [4,16,26], specific information has not
been made readily available [2] to field archaeologists
and anthropologists who are often the first to collect and
prepare human, animal or plant remains for ancient
DNA analysis. Careful contamination controls during
initial sample collection and preparation, however, can
be extremely effective in minimizing the risk of false
positive results.
This paper discusses the nature of contamination in
ancient DNA studies, proposes a series of precautions
for excavating and subsequent processing of ancient
remains intended for ancient DNA analysis, and offers
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D.Y. Yang, K. Watt / Journal of Archaeological Science 32 (2005) 331–336
some suggestions for the proper preparation of previously excavated samples for DNA analysis.
can be applied to answer archaeological and anthropological questions [16,26,36].
2. Contamination in ancient DNA studies
3. Sources of contamination
Two major problems associated with the study of
ancient DNA are the degradation of DNA over time
and the contamination of ancient samples with modern
DNA [11,15,22]. Physical and chemical degradation can
destroy most of the DNA molecules contained in
ancient remains. The minute amounts of preserved
DNA are left in poor condition, damaged and broken
into small pieces, causing difficulties in the analysis of
ancient DNA molecules [18]. The invention of the
polymerase chain reaction (PCR) technique in modern
molecular biology [29] made it realistic to analyze
ancient DNA [25]. The PCR technique is an extremely
sensitive method that can detect minute amounts of
specific DNA molecules, and amplify these molecules
billions of times in a few hours [13]. PCR is an ideal tool
for detecting ancient DNA molecules since theoretically
a single molecule is enough to trigger PCR amplification. The hypersensitivity of the PCR technique, on the
other hand, also allows for contaminant DNA to be
amplified easily, generating false positive results if
inadequate amounts of ancient DNA template are
available. Although contamination concerns are associated with all PCR-based DNA analyses, including
modern DNA work, due to the availability of adequate
amounts of modern DNA molecules, the target DNA
usually outnumbers the contaminant DNA. As a result,
contamination may have insignificant or little impact on
the analysis of modern DNA. However, due to the
degradation of ancient DNA, the authentic template can
be overwhelmed by contaminant DNA if effective
contamination controls are not set in place [35]. As
a matter of fact, contamination has been found to be
responsible for the erroneously claimed positive PCR
amplification of the alleged Dinosaur DNA and other
million year-old DNA [1,10].
The high risk of contamination in ancient DNA
studies can be better illustrated through the following
example. While there are likely only a few thousand
copies of mtDNA housed in ancient remains, one simple
touch of the researchers’ hand on ancient human
remains can leave many shed skin cells, each of which
can contain 1000 copies of mtDNA. In this case,
contaminant human mtDNA easily outnumbers the
authentic ancient DNA; PCR is more likely to amplify
the contaminant DNA, resulting in false positive
amplification.
Due to the increased risk of contamination in ancient
DNA studies, the possibility of contamination must be
thoroughly examined. The authenticity of the DNA
must be carefully evaluated before ancient DNA results
In a strict sense, the terms ‘‘contaminant DNA’’ and
‘‘contamination’’ in ancient DNA studies do not refer to
the mixing of chemical impurities with ancient DNA
samples, as they do in chemistry. Contaminant DNA
refers to DNA that is identical or similar to the target
ancient DNA which could be indiscriminately amplified
by PCR. For example, bacterial and fungal DNA
present in ancient human DNA samples (they make
up the majority of total extracted DNA from remains
[9]) should not be considered contaminant DNA if
research targets ancient human DNA.
Sources of contamination vary considerably depending on the type of ancient remains and the types of
research questions being posed:
1. In ancient human DNA studies, contaminant DNA
can come from individuals who excavate, study and
handle the remains as well as those who manufacture
laboratory supplies such as chemical reagents and
even test tubes [6,12,35].
2. For ancient faunal and floral DNA studies, contamination would most likely originate from modern
reference specimens that are used for detailed oneto-one comparisons during morphological identifications of the remains [36]. Human DNA should not
be considered a contamination source if distinctive
PCR primers for ancient faunal and floral DNA
studies are carefully chosen.
3. For ancient pathogenic DNA studies of bacterial
species, contaminant DNA may also come from
closely related species in soils and surrounding
environments [8] (soil samples should therefore be
collected in order to determine whether soils contain
closely related species). PCR techniques should also
be specifically designed to use those DNA markers
that can distinguish target pathogenic species from
possible contaminant species.
For ancient remains of certain antiquity (several
thousands of years, for example), cross-sample contamination between ancient remains themselves may not be
a severe problem since only a minute amount of DNA is
preserved (at best) in the remains. Strict sample-tosample controls, however, should still be in place as
a precaution and also as a measure to stop surface
contaminant DNA appearing on one sample from
passing on to the next sample.
Obviously, the largest potential contamination source
is the PCR products of previous PCR amplifications
of the same or closely related species [11,12]. The
D.Y. Yang, K. Watt / Journal of Archaeological Science 32 (2005) 331–336
prevention of such contamination is wholly dependent
upon the availability of a dedicated ancient DNA laboratory and the careful performance of experiments in an
ancient DNA laboratory [26].
4. What ancient DNA researchers do for
in-laboratory contamination controls
We use the term ‘‘in-laboratory contamination
controls’’ to refer to the strict precautions and measures
that are exercised in an ancient DNA laboratory. In
spite of being seemingly directed towards ancient DNA
researchers, we believe that the following discourse is
useful to help our readers gain an understanding of the
vigorousness of in-laboratory contamination control
measures. We hope that this discussion will help field
archaeologists appreciate the importance of pre-laboratory contamination controls in contributing to the
overall success of ancient DNA studies.
For effective in-laboratory contamination controls,
a dedicated ancient DNA laboratory is required: (1) to
extract DNA from ancient samples (no modern DNA
should be processed in this laboratory); (2) to prevent
amplified PCR products from entering into the DNA
extraction process and mixing with ancient DNA
samples; (3) to prevent contamination from other
samples that are being processed or those that have
been processed previously in the laboratory; and (4)
when working on ancient human DNA, to prevent
ancient DNA laboratory technicians from shedding
their own DNA into ancient DNA samples.
Several other precautionary measures should also be
set in place to effectively implement contamination
controls. In dedicated ancient DNA laboratories,
ideally, equipment and rooms should be set up for the
exclusive purposes of bone preparation, DNA extraction and PCR setup. PCR amplifications must be
conducted in a physically separated PCR laboratory or
area; this simple guideline has proven to be one of the
most effective contamination controls [4,11]. In the
ancient DNA laboratory, air should be UV-HEPAfiltered and positively pressurized, UV irradiation
should be used to destroy possible DNA residues on
bench and equipment surfaces after being wiped with
bleach, and laboratory technicians should wear protective suits, gloves and masks to protect samples from
being contaminated.
If all in-laboratory contamination controls are in
place, the possibility of contamination during the
ancient DNA lab process should be significantly reduced. Unfortunately, these controls cannot annul
contamination that occurred prior to the ancient
remains being sent to the ancient DNA laboratory. To
a certain degree, most archaeological remains currently
kept in museums and universities are contaminated [28].
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When archaeologists excavated those remains 20 years
ago, it is unlikely that they wore protective suites, gloves
and masks, anticipating the advent of ancient DNA
analysis in the future. Even if these remains were not
contaminated during excavation, subsequent laboratory
analyses of specimen-to-specimen comparison would
likely have resulted in such contamination.
Such pre-laboratory contamination can be a serious
problem for ancient DNA studies. As a ‘‘damage
control’’, ancient DNA laboratories have had to use
a variety of methods to remove contaminant DNA from
ancient remains. These decontamination processes include physical removal of the contaminated surface of
ancient materials or chemical destructions of contaminant DNA that may have penetrated into bone tissues
[36]. Decontamination by nature is destructive and each
method has different levels of effectiveness. Each
specimen has a unique history of excavation and
storage, and levels of contamination can vary considerably. Therefore, there is no means to guarantee complete
removal of contaminant DNA through decontamination
procedures. If decontamination is too destructive, it may
also destroy too much of the authentic DNA that has
fortunately survived to date. If decontamination is not
adequate, contaminant DNA may not be thoroughly
removed. Ancient DNA researchers must make balanced
decisions concerning decontamination protocols and
then implement complex research designs to identify
contamination should it occur. The whole process is
labor-intensive and time-consuming [16].
5. Pre-laboratory contamination controls by field
archaeologists
5.1. Clean collection of samples during excavation
Effective pre-laboratory contamination controls by
field archaeologists and subsequent lab workers can be
most valuable in the success of overall contamination
controls. Logically, contamination controls should be in
place at the moment ancient remains are unearthed from
the ground. Ideally, controls in the field should be as
strict as the in-laboratory measures; however, outdoor
excavation conditions may prevent such strict contamination controls. There are some general guidelines that
should be followed during excavation and subsequent
storage of samples that will minimize the chance of
contamination.
1. Do not attempt to clean specimens designated for
ancient DNA analysis, dirt on the specimens may
serve as protection against contaminants entering
into bone tissues, making in-laboratory decontamination easier.
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D.Y. Yang, K. Watt / Journal of Archaeological Science 32 (2005) 331–336
2. Do not wash specimens as water may cause
contaminant DNA to penetrate deeply into bone
tissues and may also cause hydrolytic damage to
ancient DNA.
3. If possible, avoid adding any preservatives to
specimens as these chemicals may inhibit PCR
amplifications and may cause potential contaminant
DNA to adhere to the specimens [21].
4. Store specimens in cool, dry conditions to avoid
further degradation of ancient DNA.
5. Store ancient specimens separately from modern
reference specimens to prevent cross-sample contamination.
6. If possible, change gloves and clean or change tools
from one specimen to another when handling.
Specimens should be individually stored in plastic
bags or tubes but only when they are completely dry.
Otherwise, a paper bag should be used.
Field archaeologists and anthropologists should
evaluate the possibility of collecting specimens for
ancient DNA analysis in advance and prepare the
required tools for clean collection. Unfortunately, it is
unrealistic to expect that field archaeologists would be
equipped with the same set of protective suits as ancient
DNA technicians working in a dedicated laboratory
environment. However, the use of common sense in
clean collection should be applied. Generally, an ancient
DNA sample collection ‘‘kit’’ should include disposable
gloves, clean paper bags, aluminum foil, masks, hairnets, sealable plastic bags, bleach solution and clean
excavation tools such as trowels and dental picks. For
non-disposable tools, use a 10% commercial bleach
solution for cleansing between samples (bleach has been
found to be effective in ‘‘damaging’’ DNA [28]).
(Unpublished data from our own lab and others
indicated higher concentrations of bleach might be
needed for more effective decontamination.) The clean
collection tool-kit does not have to be sterile, but needs
to be kept clean. Keep in mind that the same disposable
tool should not be used for more than one sample or one
skeleton.
An understanding of DNA preservation can also be
useful when selecting ancient remains for DNA analysis
[18]. Generally, ancient remains that date to within the
last ten thousand years deserve serious consideration for
ancient DNA analysis. However, in some cold regions,
such as Arctic and Sub-arctic areas, materials for DNA
analysis can be much older [30,34]. When selecting
specimens, one should choose morphologically wellpreserved specimens in the following order: teeth,
cortical bone, and finally spongy bone. A small amount
of bone (1–2 g) or one tooth is usually adequate for one
ancient DNA extraction. For reproducibility tests,
a second set of samples (bone or a tooth) should also
be collected.
Special care should always be taken when collecting
human samples for DNA analysis. If it is impossible for
all personnel to take protective measures for the entire
excavation, it should be reasonable for a couple of
excavators to do so for the short periods of time
required to collect the samples. Not all remains will
undergo DNA analysis, therefore as a compromise, only
a small number of samples need to be collected under
strict contamination controls. In most cases, a few small
bones (hand and foot bones, for example), fragmentary
pieces of bone, or teeth should be sufficient for such
analysis. However, due to the destructive nature of
ancient DNA analysis, bones should not be selected if
they also hold potential for morphological and pathological examinations [5]. If possible, multiple pieces of
samples should be collected for reproducibility tests.
When the selected bones are collected, they should be
wrapped in aluminum foil (not sealed) and put into
a clean paper bag for natural drying. If wet, they should
not be placed into a sealed plastic bag as moisture sealed
in a bag will create ideal conditions for bacteria growth,
which will cause further degradation to ancient materials and ancient DNA through endogenous (autolytic)
and microbial nuclease activities. Ancient materials,
however, can be sealed in a plastic bag such as ZiplocÔ
when materials are completely dry.
Burial environment can provide some useful clues
about DNA preservation. If possible, one should collect
other animal and plant species in addition to soil
samples. This will allow for examination of soil
chemistry which may shed some light on DNA
degradation rates as well as the DNA preservation of
other taxa. Although the main research focus may just
be on ancient human DNA, DNA from other species
collected at the site can be used later as secondary
evidence for the authenticity of the human DNA [26]. If
one succeeds in retrieving ancient human DNA but not
animal DNA from the same site, the possibility of
human DNA contamination should be examined with
extra care.
When transporting the samples to the laboratory
from the field, the designated specimens for DNA
analysis should be stored in cool, dry conditions. For
ancient human DNA analysis, researchers and previous
field excavators should make their hair samples (with
roots) or buccal swab samples available for DNA
extraction and subsequent comparison with the studied
human remains. These reference samples should also be
sealed individually in separate clean test tubes.
When small bone elements or bone fragments are
available, there is no need to cut them into smaller pieces
if sample conservation is not a major concern. These
bones can be simply shipped to an ancient DNA
laboratory for sampling and the remaining portion can
be returned. If a bone sample needs to be cut into
smaller pieces, cortical bones should be chosen over
D.Y. Yang, K. Watt / Journal of Archaeological Science 32 (2005) 331–336
spongy bones; cortical bone is less porous, and therefore
less vulnerable to contaminant DNA. The dense texture
of cortical bones also provides a more protective milieu
for DNA, making more ancient DNA molecules available for analysis.
5.2. Old materials from previous excavations
Previously excavated archaeological remains hold
great potential for ancient DNA studies. Some of these
samples may have been under intensive and extensive
archaeological or anthropological studies prior to the
decision to undertake ancient DNA analysis. The
retrieval and analysis of ancient DNA from these
remains may prove to be challenging due to the
likelihood that most of these samples have been
contaminated with modern DNA. For ancient human
remains, it is difficult for one to trace the record of when
they were handled and who studied the materials,
making the collection of reference DNA samples from
all previous researchers virtually impossible. This is an
unfortunate reality, and it is essential to rely on ancient
DNA lab technicians to conduct effective decontamination procedures inside the laboratory. A brief history of
research conducted on the bone samples (such as when
they were handled and how many people have handled
them, and the accuracy of the records), if available, will
be very helpful for ancient DNA technicians to decide
which decontamination strategy should be used. Essentially, there is no need for field archaeologists or
anthropologists to perform any decontamination measures since these practices, if not well controlled, may
introduce new contaminant DNA into the samples.
The primary concern when selecting and preparing
contaminated specimens for ancient DNA analysis is the
avoidance of cross-sample contamination, specifically
during the cutting of appropriate sample quantities. A
small hacksaw should be used to cut long bones into
small pieces of 1–2 cm. A new hacksaw blade should be
used for each sample. Blades can be reused only after
they are cleaned with detergent and wiped with a bleach
solution. Dremel tools and drills can also be used and
cleaned in similar ways, however low speeds should be
used to prevent bone dust from spreading. The bench or
table surface should be wiped with bleach solution and
padded with new sheets of paper towel after every
individual sample is processed. Each processed sample
should then be individually stored in a sealable plastic
bag, so long as it is dry.
335
can help facilitate this objective. When preparing
samples for ancient DNA analysis, all morphological
and other identification information should be removed
and the samples should be re-numbered; mock sample(s)
(related species of animals and plants, or unrelated
human skeletal remains) should also be incorporated
into the sample set. The mock samples are those known
samples (to archaeologists only) that are intentionally
labeled as ‘‘legitimate’’ samples and mixed with study
materials by archaeologists. Ancient DNA analysis
should distinguish these mock samples from real study
samples due to their anomalous DNA sequences. Success
in doing so demonstrates the effectiveness of contamination controls and the reliability of ancient DNA
analysis. The cross-examination resulting from the blind
test is very informative for detecting contaminant DNA
or for authenticating ancient DNA samples [36].
7. ‘‘Common sense works’’
After consultation with field archaeologists, the
authors have found that it is almost impossible to
develop universal protocols that will suit all excavation
situations and all types of ancient remains. As a result,
this paper is not intended to provide highly specific and
detailed procedures for contamination controls. Once
the importance of contamination controls is realized and
all possible contamination sources are identified, one
can follow the ‘‘common sense’’ approach.
8. Other issues
1. This paper presents general guidelines for contamination controls for sample collection and preparation. However, field archaeologists are strongly
encouraged to contact their potential ancient DNA
collaborators for updated information and alternate
measures for contamination controls.
2. The destructive nature of ancient DNA analysis may
require ethical approval for DNA studies of human
remains [15]. The collection of the comparative DNA
samples also needs informed consents from crew
members.
3. Ancient DNA preservation varies considerably from
site to site, a pilot project of a few samples (3–5)
should be conducted first to evaluate the state of
preservation before a large number of samples are
collected and prepared.
6. Blind test
Acknowledgements
We advocate the implementation of blind tests in all
ancient DNA studies (whenever possible) to aid in
contamination detection [36,37]. Field archaeologists
Our special thanks go to Camilla Speller for reading
and commenting on the draft of the manuscript. We
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D.Y. Yang, K. Watt / Journal of Archaeological Science 32 (2005) 331–336
thank Alice Storey for discussion. We also want to
thank three anonymous reviewers for their constructive
comments that have greatly improved the quality of this
manuscript. This research was supported in part by
Social Science and Humanities Research Council of
Canada.
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